LAMMPS (24 Dec 2020)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:97)
  using 1 OpenMP thread(s) per MPI task
# Big colloid particles and small LJ particles

units		lj
atom_style	sphere
dimension	2

lattice		sq 0.5
Lattice spacing in x,y,z = 1.4142136 1.4142136 1.4142136
region		box block 0 60 0 60 -0.5 0.5
create_box	2 box
Created orthogonal box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678)
  1 by 1 by 1 MPI processor grid
create_atoms	1 box
Created 3600 atoms
  create_atoms CPU = 0.001 seconds
change_box      all triclinic
Changing box ...
  triclinic box = (0.0000000 0.0000000 -0.70710678) to (84.852814 84.852814 0.70710678) with tilt (0.0000000 0.0000000 0.0000000)

# remove two spheres of small particles and add large particles in the voids
region sphere1 sphere 20.0 20.0 0.0 10.0 units box
region sphere2 sphere 60.0 60.0 0.0 10.0 units box
delete_atoms  region sphere1
Deleted 154 atoms, new total = 3446
delete_atoms  region sphere2
Deleted 158 atoms, new total = 3288
create_atoms 2 single 20.0 20.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds
create_atoms 2 single 60.0 60.0 0.0 units box
Created 1 atoms
  create_atoms CPU = 0.000 seconds

set		type 2 mass 400
Setting atom values ...
  2 settings made for mass
set		type 1 mass 1
Setting atom values ...
  3288 settings made for mass
set     type 2 diameter 20
Setting atom values ...
  2 settings made for diameter
set     type 1 diameter 1
Setting atom values ...
  3288 settings made for diameter

velocity	all create 1.44 87287 loop geom

# multi neighbor and comm for efficiency

neighbor	1 multi #multi/old
neigh_modify	delay 0 collection/interval 2 1 20
comm_modify     mode multi vel yes reduce/multi #multi/old

# colloid potential

pair_style      granular
pair_coeff      * * hooke 1.0 0.5 tangential linear_history 1.0 0.5 0.1 damping mass_velocity

fix		1 all nph/sphere iso 0.0 1.0 10.0 drag 1.0
fix		2 all enforce2d
fix             3 all deform 1 xy erate 1e-3

#dump		1 all custom 1000 dump.granular id x y z radius

#dump		2 all image 1000 image.*.jpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	2 pad 5 adiam 1 5.0 adiam 2 1.5

#dump		3 all movie 1000 movie.mpg type type #		zoom 1.5 center d 0.5 0.5 0.5
#dump_modify	3 pad 5 adiam 1 5.0 adiam 2 1.5

thermo_style	custom step temp epair etotal press vol
thermo		1000

timestep	0.005

run		50000
Neighbor list info ...
  update every 1 steps, delay 0 steps, check yes
  max neighbors/atom: 2000, page size: 100000
  master list distance cutoff = 21
  ghost atom cutoff = 21
  binsize = 1, bins = 85 85 2
  1 neighbor lists, perpetual/occasional/extra = 1 0 0
  (1) pair granular, perpetual
      attributes: half, newton on, size, history
      pair build: half/size/multi/newton/tri
      stencil: half/multi/2d/tri
      bin: multi
Per MPI rank memory allocation (min/avg/max) = 10.29 | 10.29 | 10.29 Mbytes
Step Temp E_pair TotEng Press Volume 
       0         1.44            0    1.4395623   0.66837658         7200 
    1000   0.32604952            0   0.32595042   0.17341597    7862.5013 
    2000   0.12631038            0   0.12627198  0.069126477    8216.6956 
    3000  0.069351715            0  0.069330635  0.040799593    8344.1931 
    4000  0.045023755            0   0.04501007  0.029184795    8239.1832 
    5000  0.032735149            0    0.0327252  0.025640841    7943.5691 
    6000  0.026205227            0  0.026197262  0.021206924    7617.6672 
    7000   0.02165475            0  0.021648168  0.018789365    7255.2897 
    8000  0.018299317            0  0.018293755  0.019272158    6887.3386 
    9000  0.016283763            0  0.016278813  0.020434892    6524.0274 
   10000  0.015148918            0  0.015144313  0.021650465    6168.4941 
   11000  0.014180465            0  0.014176155  0.022320009      5823.98 
   12000  0.013505744            0  0.013501639  0.023978674    5492.4853 
   13000  0.013009585            0   0.01300563  0.024391329    5175.7455 
   14000  0.012494373            0  0.012490576  0.027331543    4874.3212 
   15000  0.012057669            0  0.012054004  0.030561239     4589.518 
   16000  0.011510988            0   0.01150749  0.034613772    4321.1694 
   17000  0.011198594            0   0.01119519  0.042263536    4070.0115 
   18000  0.010978603            0  0.010975266  0.053637275    3836.0304 
   19000  0.010768789            0  0.010765516  0.069472547      3619.75 
   20000    0.0102256            0  0.010222492  0.085332898    3420.2738 
   21000 0.0089630315            0 0.0089603072   0.11199196    3236.9821 
   22000  0.006565581            0 0.0065635854   0.14807426    3071.3012 
   23000 0.0050916998            0 0.0050901522    0.1903446    2923.4162 
   24000 0.0040345997            0 0.0040333734     0.237983    2792.2658 
   25000 0.0032995328            0 0.0032985299   0.29120001    2677.7475 
   26000 0.0024157863            0  0.002415052   0.33851944    2578.4972 
   27000 0.0020664445            0 0.0020658164   0.37561848    2491.0264 
   28000 0.0017843883            0 0.0017838459   0.41119961    2412.3871 
   29000 0.0011813262            0 0.0011809672   0.44749341    2341.7208 
   30000 0.00063084711            0 0.00063065536    0.4879202    2279.0452 
   31000 0.00056027405            0 0.00056010376   0.52932126    2224.9456 
   32000 0.00053304715            0 0.00053288513   0.56822504    2179.1224 
   33000 0.00052245707            0 0.00052229826   0.60025509    2140.5345 
   34000 0.00073726189            0 0.0007370378   0.62001489    2106.3045 
   35000 0.00075804791            0 0.0007578175    0.6359631     2072.525 
   36000 0.00052579203            0 0.00052563222   0.65678516    2038.1907 
   37000 0.00036977909            0 0.0003696667   0.68784389    2005.5831 
   38000 0.00036252798            0 0.00036241779   0.72116044    1977.7441 
   39000 0.00036254566            0 0.00036243547   0.74720837    1954.9127 
   40000 0.00036237175            0 0.00036226161   0.76605408    1934.6006 
   41000 0.00032453104            0 0.00032443239   0.78424188    1914.1939 
   42000 0.00025394755            0 0.00025387036   0.80529272     1893.064 
   43000 0.00021067821            0 0.00021061418   0.82962095     1872.365 
   44000 0.00017927684            0 0.00017922235   0.85522899     1853.531 
   45000 0.0001464225            0  0.000146378   0.87925998    1837.2423 
   46000 0.00012922979            0 0.00012919051    0.8986549    1822.9227 
   47000 0.0001643557            0 0.00016430575   0.91743602    1809.0605 
   48000 0.00020154753            0 0.00020148627   0.93686779    1794.9227 
   49000 0.00017742528            0 0.00017737135   0.94988773    1780.3811 
   50000 0.00015150521            0 0.00015145916   0.97929588    1764.7507 
Loop time of 54.9135 on 1 procs for 50000 steps with 3290 atoms

Performance: 393345.914 tau/day, 910.523 timesteps/s
100.0% CPU use with 1 MPI tasks x 1 OpenMP threads

MPI task timing breakdown:
Section |  min time  |  avg time  |  max time  |%varavg| %total
---------------------------------------------------------------
Pair    | 44.691     | 44.691     | 44.691     |   0.0 | 81.38
Neigh   | 0.21653    | 0.21653    | 0.21653    |   0.0 |  0.39
Comm    | 0.75388    | 0.75388    | 0.75388    |   0.0 |  1.37
Output  | 0.0011999  | 0.0011999  | 0.0011999  |   0.0 |  0.00
Modify  | 8.4718     | 8.4718     | 8.4718     |   0.0 | 15.43
Other   |            | 0.7794     |            |       |  1.42

Nlocal:        3290.00 ave        3290 max        3290 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost:        525.000 ave         525 max         525 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs:        26732.0 ave       26732 max       26732 min
Histogram: 1 0 0 0 0 0 0 0 0 0

Total # of neighbors = 26732
Ave neighs/atom = 8.1252280
Neighbor list builds = 342
Dangerous builds = 0

Please see the log.cite file for references relevant to this simulation

Total wall time: 0:00:54
